Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation

Gemma Fisher; Marina Corbella; Magnus Stephen Alphey; John Nicholson; Benjamin Read; Shina C. L.  Kamerlin; R.G.  da Silva

doi:10.1038/s41467-022-34960-9

Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation

Gemma Fisher, Marina Corbella, Magnus Stephen Alphey, John Nicholson, Benjamin Read, Shina C. L. Kamerlin^*, R.G. da Silva^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

ATP phosphoribosyltransferase catalyses the first step of histidine biosynthesis and is controlled via a complex allosteric mechanism where the regulatory protein HisZ enhances catalysis by the catalytic protein HisG_S while mediating allosteric inhibition by histidine. Activation by HisZ was proposed to position HisG_S Arg56 to stabilise departure of the pyrophosphate leaving group. Here we report active-site mutants of HisG_S with impaired reaction chemistry which can be allosterically restored by HisZ despite the HisZ:HisG_S interface lying ~20 Å away from the active site. MD simulations indicate HisZ binding constrains the dynamics of HisGS to favour a preorganised active site where both Arg56 and Arg32 are poised to stabilise leaving-group departure in WT-HisG_S. In the Arg56Ala-HisG_S mutant, HisZ modulates Arg32 dynamics so that it can partially compensate for the absence of Arg56. These results illustrate how remote protein-protein interactions translate into catalytic resilience by restoring damaged electrostatic preorganisation at the active site.

Original language	English
Article number	7607
Number of pages	15
Journal	Nature Communications
Volume	13
DOIs	https://doi.org/10.1038/s41467-022-34960-9
Publication status	Published - 9 Dec 2022

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Fisher_2022_NC_Allosteric-resscue_CC
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Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation (dataset 2)
Fisher, G. (Creator), Corbella, M. (Creator), Alphey, M. S. (Creator), Nicholson, J. (Creator), Read, B. (Creator) & Guimaraes da Silva, R. (Creator), Zenodo, 2022
DOI: 10.5281/zenodo.7077771
Dataset
Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation (dataset)
Alphey, M. S. (Creator), Read, B. (Creator) & Guimaraes da Silva, R. (Creator), Protein Data Bank archive (PDB), 2022
DOI: 10.2210/pdb7Z8U/pdb, https://www.rcsb.org/structure/6FCT and 2 more links, https://www.rcsb.org/structure/6FU2, https://www.rcsb.org/structure/7Z6R (show fewer)
Dataset
digest data
Shirran, S. (Creator) & Guimaraes da Silva, R. (Creator), Figshare, 2022
DOI: 10.6084/m9.figshare.19658367.v1
Dataset

Cite this

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title = "Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation",

abstract = "ATP phosphoribosyltransferase catalyses the first step of histidine biosynthesis and is controlled via a complex allosteric mechanism where the regulatory protein HisZ enhances catalysis by the catalytic protein HisGS while mediating allosteric inhibition by histidine. Activation by HisZ was proposed to position HisGS Arg56 to stabilise departure of the pyrophosphate leaving group. Here we report active-site mutants of HisGS with impaired reaction chemistry which can be allosterically restored by HisZ despite the HisZ:HisGS interface lying ~20 {\AA} away from the active site. MD simulations indicate HisZ binding constrains the dynamics of HisGS to favour a preorganised active site where both Arg56 and Arg32 are poised to stabilise leaving-group departure in WT-HisGS. In the Arg56Ala-HisGS mutant, HisZ modulates Arg32 dynamics so that it can partially compensate for the absence of Arg56. These results illustrate how remote protein-protein interactions translate into catalytic resilience by restoring damaged electrostatic preorganisation at the active site.",

author = "Gemma Fisher and Marina Corbella and Alphey, {Magnus Stephen} and John Nicholson and Benjamin Read and Kamerlin, {Shina C. L.} and {da Silva}, R.G.",

note = "Funding: This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) [Grant BB/M010996/1] via EASTBIO Doctoral Training Partnership studentships to B. J. R. and G. F., by Stiftelsen Olle Engkvist Byggm{\"a}stare [Grant 190-0335] and the Knut and Alice Wallenberg Foundation [Grants 2018.0140 and 2019.0431] to S.C.L.K., and by the European Union{\textquoteright}s Horizon 2020 Research and Innovation Programme via a Marie Sklodowska-Curie fellowship [Grant 890562] to M.C. The simulations were enabled by resources provided by the Swedish National Infrastructure for Supercomputing (SNIC, UPPMAX), partially funded by the Swedish Research Council [Grant 2016-07213].",

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AU - Fisher, Gemma

AU - Corbella, Marina

AU - Alphey, Magnus Stephen

AU - Nicholson, John

AU - Read, Benjamin

AU - Kamerlin, Shina C. L.

AU - da Silva, R.G.

N1 - Funding: This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) [Grant BB/M010996/1] via EASTBIO Doctoral Training Partnership studentships to B. J. R. and G. F., by Stiftelsen Olle Engkvist Byggmästare [Grant 190-0335] and the Knut and Alice Wallenberg Foundation [Grants 2018.0140 and 2019.0431] to S.C.L.K., and by the European Union’s Horizon 2020 Research and Innovation Programme via a Marie Sklodowska-Curie fellowship [Grant 890562] to M.C. The simulations were enabled by resources provided by the Swedish National Infrastructure for Supercomputing (SNIC, UPPMAX), partially funded by the Swedish Research Council [Grant 2016-07213].

PY - 2022/12/9

Y1 - 2022/12/9

N2 - ATP phosphoribosyltransferase catalyses the first step of histidine biosynthesis and is controlled via a complex allosteric mechanism where the regulatory protein HisZ enhances catalysis by the catalytic protein HisGS while mediating allosteric inhibition by histidine. Activation by HisZ was proposed to position HisGS Arg56 to stabilise departure of the pyrophosphate leaving group. Here we report active-site mutants of HisGS with impaired reaction chemistry which can be allosterically restored by HisZ despite the HisZ:HisGS interface lying ~20 Å away from the active site. MD simulations indicate HisZ binding constrains the dynamics of HisGS to favour a preorganised active site where both Arg56 and Arg32 are poised to stabilise leaving-group departure in WT-HisGS. In the Arg56Ala-HisGS mutant, HisZ modulates Arg32 dynamics so that it can partially compensate for the absence of Arg56. These results illustrate how remote protein-protein interactions translate into catalytic resilience by restoring damaged electrostatic preorganisation at the active site.

AB - ATP phosphoribosyltransferase catalyses the first step of histidine biosynthesis and is controlled via a complex allosteric mechanism where the regulatory protein HisZ enhances catalysis by the catalytic protein HisGS while mediating allosteric inhibition by histidine. Activation by HisZ was proposed to position HisGS Arg56 to stabilise departure of the pyrophosphate leaving group. Here we report active-site mutants of HisGS with impaired reaction chemistry which can be allosterically restored by HisZ despite the HisZ:HisGS interface lying ~20 Å away from the active site. MD simulations indicate HisZ binding constrains the dynamics of HisGS to favour a preorganised active site where both Arg56 and Arg32 are poised to stabilise leaving-group departure in WT-HisGS. In the Arg56Ala-HisGS mutant, HisZ modulates Arg32 dynamics so that it can partially compensate for the absence of Arg56. These results illustrate how remote protein-protein interactions translate into catalytic resilience by restoring damaged electrostatic preorganisation at the active site.

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Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation

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Datasets

Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation (dataset 2)

Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation (dataset)

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